Hi there,
I am using ckedtior 3.6.2 with PeopleTools 8.52 and toolbar Style/ Formats/Fonts/Size list are showing balnk in IE 9. Earlier I was using 3.5.3 version and I had the same problem. After reading the below note I upgrade the version up to 3.6.2 but still having the same problem.
http://ckeditor.com/forums/CKEditor-3.x/IE-9-Issue-fontstyleSizeFormat-list
With Peopletools 8.49 , ckeditor 3.5.3 version is working fine in IE 9.